BtaINT0148055 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047673 | THUMPD1
Description
Bos taurus THUMP domain containing 1 (THUMPD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001046277]
Coordinates
chr25:18566260-18567854:-
Coord C1 exon
chr25:18567606-18567854
Coord A exon
chr25:18566793-18567605
Coord C2 exon
chr25:18566260-18566792
Length
813 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TGTTTTCCTTTTTGTTACAGGAA
3' ss Score
11.39
Exon sequences
Seq C1 exon
AACCTGAGAAATTGGTGCATCATATTCTCCAAGATATATACAAAACCAAGAAGAAGAAGACTCGGGTTATTCTACGAATGTTGCCCATCTCAGGCACATGCAAGGCTTTCTTAGAAGATATGAAAAAATATGCAGAAACATTTTTGGAACCATGGTTTAAAGCTCCAAACAAAGGAACATTTCAGATTGTATACAAATCTCGGAATAACAGTCATATGAATAGAGAAGAAGTTATCAAAGAATTGGCAG
Seq A exon
GTATGTTTCTCTTAGTGATTTTGCAAAGATGTGCCATGGTAAATATTTGCTTTTAAGATTTTTTTTTTTTTTAATATTTAGGGCTTATATTTTTGAGTGAGAGCAAGTATTTTAAAATATCATTAAATAATATCAAGCCTAACTTCAATATGTTGGGTTGCTGCTGCTGCTGCTGCTAAGTCGCTTCAGTTCTGTGCGACCCCAGAGATGGCAGCCCACCAGGCTCCCCTGTCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCGCTCAGGTTGTCTACTTGAAAGTTACACAGTCATGCCGACTCCTAGCGACCCCATGGACTGCAGTCTACCAGGCTCCTCCGTCCATGGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCCATTGCCTTCTCCAAATATGTTGGGTATGAGATTATTTTTGGTAGTTAGATACTAAAGTCTTTTCCAAATCAGAATTGCATTTTCTTTGAGGAAAAAAGGGCTCTTATTAACTTTCTCAGGATTTCATTTGTATTTATGTATTGAAAGCATTCAGAAAACTTGATTCAAATACATGTAAAGTAGTGGACTAGTACATGCATTTATATATATACTATAGTATAACACTACTAATATATGTAGTGTTTCAACAACTACATTTCTGATAAGGTTAGTTATAAATTTAACAAATTCTAAATAGGGGGAGGTGAAAGATTGTTTTTGTATCCACCGAGCTTAATGGTATCTTTTTTTATCTTGTTTTCCTTTTTGTTACAG
Seq C2 exon
GAATAGTAGGCAGCCTTAATTCAGAAAATAAAGTGGATCTTAGCAATCCACAGTACACAGTGGTAGTAGAAATCATTAAAGCTGTCTGTTGCCTGAGTGTTGTGAAAGATTACATGTTGTTCAGAAAATACAATCTCCAGGAGGTGGTGAAGAGTGCTAAGGACTTGTCACAGCTTAACCCAAAGCAAGCAGCACAAACAGGAAATGGGAAAGAAGCTAAATTGGAATCTGGTGACAAATCAAGTCAAAATGACCCAGCAGAAGGAAAAAATAACCAACAAGTGGTACCAGAGAACAGTGAGGAGCTGGGTCCAACAGAATCAATATCTGAGACACATGTGGTGAATGAGGGGGTGGCTAAACCTGAACTTGCAAGTCAAGTCACAGAAGGATCTGAATCAAATGAAAATGATCTCTGATAGGAAAAGAAATTGTTTGGTGTTGGAGGTAGATGTTTCTTTTTTTTTTTGGAGGTGGATTTTTCAACTGGAGTTTTGTGAGATGTTGCTGGGATTCCATATAAAATTGTGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047673:ENSBTAT00000064153:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.597
Domain overlap (PFAM):
C1:
PF087955=DUF1796=PD(36.6=35.7),PF0292612=THUMP=FE(51.2=100)
A:
NA
C2:
PF0292612=THUMP=PD(21.6=25.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCACATGCAAGGCTTTCTT
R:
TGTGCTGCTTGCTTTGGGTTA
Band lengths:
354-1167
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]